1.
Jmol
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Jmol is computer software for molecular modelling chemical structures in 3-dimensions. Jmol returns a 3D representation of a molecule that may be used as a teaching tool and it is written in the programming language Java, so it can run on the operating systems Windows, macOS, Linux, and Unix, if Java is installed. It is free and open-source software released under a GNU Lesser General Public License version 2.0, a standalone application and a software development kit exist that can be integrated into other Java applications, such as Bioclipse and Taverna. A popular feature is an applet that can be integrated into web pages to display molecules in a variety of ways, for example, molecules can be displayed as ball-and-stick models, space-filling models, ribbon diagrams, etc. Jmol supports a range of chemical file formats, including Protein Data Bank, Crystallographic Information File, MDL Molfile. There is also a JavaScript-only version, JSmol, that can be used on computers with no Java, the Jmol applet, among other abilities, offers an alternative to the Chime plug-in, which is no longer under active development. While Jmol has many features that Chime lacks, it does not claim to reproduce all Chime functions, most notably, Chime requires plug-in installation and Internet Explorer 6.0 or Firefox 2.0 on Microsoft Windows, or Netscape Communicator 4.8 on Mac OS9. Jmol requires Java installation and operates on a variety of platforms. For example, Jmol is fully functional in Mozilla Firefox, Internet Explorer, Opera, Google Chrome, fast and Scriptable Molecular Graphics in Web Browsers without Java3D

2.
ChemSpider
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ChemSpider is a database of chemicals. ChemSpider is owned by the Royal Society of Chemistry, the database contains information on more than 50 million molecules from over 500 data sources including, Each chemical is given a unique identifier, which forms part of a corresponding URL. This is an approach to develop an online chemistry database. The search can be used to widen or restrict already found results, structure searching on mobile devices can be done using free apps for iOS and for the Android. The ChemSpider database has been used in combination with text mining as the basis of document markup. The result is a system between chemistry documents and information look-up via ChemSpider into over 150 data sources. ChemSpider was acquired by the Royal Society of Chemistry in May,2009, prior to the acquisition by RSC, ChemSpider was controlled by a private corporation, ChemZoo Inc. The system was first launched in March 2007 in a release form. ChemSpider has expanded the generic support of a database to include support of the Wikipedia chemical structure collection via their WiChempedia implementation. A number of services are available online. SyntheticPages is an interactive database of synthetic chemistry procedures operated by the Royal Society of Chemistry. Users submit synthetic procedures which they have conducted themselves for publication on the site and these procedures may be original works, but they are more often based on literature reactions. Citations to the published procedure are made where appropriate. They are checked by an editor before posting. The pages do not undergo formal peer-review like a journal article. The comments are moderated by scientific editors. The intention is to collect practical experience of how to conduct useful chemical synthesis in the lab, while experimental methods published in an ordinary academic journal are listed formally and concisely, the procedures in ChemSpider SyntheticPages are given with more practical detail. Comments by submitters are included as well, other publications with comparable amounts of detail include Organic Syntheses and Inorganic Syntheses

3.
PubChem
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PubChem is a database of chemical molecules and their activities against biological assays. The system is maintained by the National Center for Biotechnology Information, a component of the National Library of Medicine, PubChem can be accessed for free through a web user interface. Millions of compound structures and descriptive datasets can be downloaded via FTP. PubChem contains substance descriptions and small molecules with fewer than 1000 atoms and 1000 bonds, more than 80 database vendors contribute to the growing PubChem database. PubChem consists of three dynamically growing primary databases, as of 28 January 2016, Compounds,82.6 million entries, contains pure and characterized chemical compounds. Substances,198 million entries, contains also mixtures, extracts, complexes, bioAssay, bioactivity results from 1.1 million high-throughput screening programs with several million values. PubChem contains its own online molecule editor with SMILES/SMARTS and InChI support that allows the import and export of all common chemical file formats to search for structures and fragments. In the text search form the database fields can be searched by adding the name in square brackets to the search term. A numeric range is represented by two separated by a colon. The search terms and field names are case-insensitive, parentheses and the logical operators AND, OR, and NOT can be used. AND is assumed if no operator is used, example,0,5000,50,10 -5,5 PubChem was released in 2004. The American Chemical Society has raised concerns about the publicly supported PubChem database and they have a strong interest in the issue since the Chemical Abstracts Service generates a large percentage of the societys revenue. To advocate their position against the PubChem database, ACS has actively lobbied the US Congress, soon after PubChems creation, the American Chemical Society lobbied U. S. Congress to restrict the operation of PubChem, which they asserted competes with their Chemical Abstracts Service

4.
International Chemical Identifier
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Initially developed by IUPAC and NIST from 2000 to 2005, the format and algorithms are non-proprietary. The continuing development of the standard has supported since 2010 by the not-for-profit InChI Trust. The current version is 1.04 and was released in September 2011, prior to 1.04, the software was freely available under the open source LGPL license, but it now uses a custom license called IUPAC-InChI Trust License. Not all layers have to be provided, for instance, the layer can be omitted if that type of information is not relevant to the particular application. InChIs can thus be seen as akin to a general and extremely formalized version of IUPAC names and they can express more information than the simpler SMILES notation and differ in that every structure has a unique InChI string, which is important in database applications. Information about the 3-dimensional coordinates of atoms is not represented in InChI, the InChI algorithm converts input structural information into a unique InChI identifier in a three-step process, normalization, canonicalization, and serialization. The InChIKey, sometimes referred to as a hashed InChI, is a fixed length condensed digital representation of the InChI that is not human-understandable. The InChIKey specification was released in September 2007 in order to facilitate web searches for chemical compounds and it should be noted that, unlike the InChI, the InChIKey is not unique, though collisions can be calculated to be very rare, they happen. In January 2009 the final 1.02 version of the InChI software was released and this provided a means to generate so called standard InChI, which does not allow for user selectable options in dealing with the stereochemistry and tautomeric layers of the InChI string. The standard InChIKey is then the hashed version of the standard InChI string, the standard InChI will simplify comparison of InChI strings and keys generated by different groups, and subsequently accessed via diverse sources such as databases and web resources. Every InChI starts with the string InChI= followed by the version number and this is followed by the letter S for standard InChIs. The remaining information is structured as a sequence of layers and sub-layers, the layers and sub-layers are separated by the delimiter / and start with a characteristic prefix letter. The six layers with important sublayers are, Main layer Chemical formula and this is the only sublayer that must occur in every InChI. The atoms in the formula are numbered in sequence, this sublayer describes which atoms are connected by bonds to which other ones. Describes how many hydrogen atoms are connected to each of the other atoms, the condensed,27 character standard InChIKey is a hashed version of the full standard InChI, designed to allow for easy web searches of chemical compounds. Most chemical structures on the Web up to 2007 have been represented as GIF files, the full InChI turned out to be too lengthy for easy searching, and therefore the InChIKey was developed. With all databases currently having below 50 million structures, such duplication appears unlikely at present, a recent study more extensively studies the collision rate finding that the experimental collision rate is in agreement with the theoretical expectations. Example, Morphine has the structure shown on the right, as the InChI cannot be reconstructed from the InChIKey, an InChIKey always needs to be linked to the original InChI to get back to the original structure

5.
Simplified molecular-input line-entry system
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The simplified molecular-input line-entry system is a specification in form of a line notation for describing the structure of chemical species using short ASCII strings. SMILES strings can be imported by most molecule editors for conversion back into two-dimensional drawings or three-dimensional models of the molecules, the original SMILES specification was initiated in the 1980s. It has since modified and extended. In 2007, a standard called OpenSMILES was developed in the open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, the original SMILES specification was initiated by David Weininger at the USEPA Mid-Continent Ecology Division Laboratory in Duluth in the 1980s. The Environmental Protection Agency funded the project to develop SMILES. It has since modified and extended by others, most notably by Daylight Chemical Information Systems. In 2007, a standard called OpenSMILES was developed by the Blue Obelisk open-source chemistry community. Other linear notations include the Wiswesser Line Notation, ROSDAL and SLN, in July 2006, the IUPAC introduced the InChI as a standard for formula representation. SMILES is generally considered to have the advantage of being slightly more human-readable than InChI, the term SMILES refers to a line notation for encoding molecular structures and specific instances should strictly be called SMILES strings. However, the term SMILES is also used to refer to both a single SMILES string and a number of SMILES strings, the exact meaning is usually apparent from the context. The terms canonical and isomeric can lead to confusion when applied to SMILES. The terms describe different attributes of SMILES strings and are not mutually exclusive, typically, a number of equally valid SMILES strings can be written for a molecule. For example, CCO, OCC and CC all specify the structure of ethanol, algorithms have been developed to generate the same SMILES string for a given molecule, of the many possible strings, these algorithms choose only one of them. This SMILES is unique for each structure, although dependent on the algorithm used to generate it. These algorithms first convert the SMILES to a representation of the molecular structure. A common application of canonical SMILES is indexing and ensuring uniqueness of molecules in a database, there is currently no systematic comparison across commercial software to test if such flaws exist in those packages. SMILES notation allows the specification of configuration at tetrahedral centers, and these are structural features that cannot be specified by connectivity alone and SMILES which encode this information are termed isomeric SMILES

6.
Chemical formula
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These are limited to a single typographic line of symbols, which may include subscripts and superscripts. A chemical formula is not a name, and it contains no words. Although a chemical formula may imply certain simple chemical structures, it is not the same as a full chemical structural formula. Chemical formulas can fully specify the structure of only the simplest of molecules and chemical substances, the simplest types of chemical formulas are called empirical formulas, which use letters and numbers indicating the numerical proportions of atoms of each type. Molecular formulas indicate the numbers of each type of atom in a molecule. For example, the formula for glucose is CH2O, while its molecular formula is C6H12O6. This is possible if the relevant bonding is easy to show in one dimension, an example is the condensed molecular/chemical formula for ethanol, which is CH3-CH2-OH or CH3CH2OH. For reasons of structural complexity, there is no condensed chemical formula that specifies glucose, chemical formulas may be used in chemical equations to describe chemical reactions and other chemical transformations, such as the dissolving of ionic compounds into solution. A chemical formula identifies each constituent element by its chemical symbol, in empirical formulas, these proportions begin with a key element and then assign numbers of atoms of the other elements in the compound, as ratios to the key element. For molecular compounds, these numbers can all be expressed as whole numbers. For example, the formula of ethanol may be written C2H6O because the molecules of ethanol all contain two carbon atoms, six hydrogen atoms, and one oxygen atom. Some types of compounds, however, cannot be written with entirely whole-number empirical formulas. An example is boron carbide, whose formula of CBn is a variable non-whole number ratio with n ranging from over 4 to more than 6.5. When the chemical compound of the consists of simple molecules. These types of formulas are known as molecular formulas and condensed formulas. A molecular formula enumerates the number of atoms to reflect those in the molecule, so that the formula for glucose is C6H12O6 rather than the glucose empirical formula. However, except for very simple substances, molecular chemical formulas lack needed structural information, for simple molecules, a condensed formula is a type of chemical formula that may fully imply a correct structural formula. For example, ethanol may be represented by the chemical formula CH3CH2OH

7.
Natural product
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A natural product is a chemical compound or substance produced by a living organism—that is, found in nature. In the broadest sense, natural products include any substance produced by life, natural products can also be prepared by chemical synthesis and have played a central role in the development of the field of organic chemistry by providing challenging synthetic targets. The term natural product has also extended for commercial purposes to refer to cosmetics, dietary supplements. Within the field of chemistry, the definition is often further restricted to secondary metabolites. Secondary metabolites are not essential for survival, but nevertheless provide organisms that produce them an evolutionary advantage, many secondary metabolites are cytotoxic and have been selected and optimized through evolution for use as chemical warfare agents against prey, predators, and competing organisms. Natural products sometimes have pharmacological or biological activity that can be of benefit in treating diseases. As such, natural products are the active components not only of most traditional medicines, in fact, natural products are the inspiration for approximately one half of U. S. Food and Drug Administration-approved drugs. The broadest definition of natural product is anything that is produced by life, and includes the likes of biotic materials, bio-based materials, bodily fluids, a more restrictive definition of a natural product is an organic compound that is synthesized by a living organism. The remainder of this article restricts itself to this more narrow definition, natural products may be classified according to their biological function, biosynthetic pathway, or source as described below. Following Albrecht Kossels original proposal in 1891, natural products are divided into two major classes, the primary and secondary metabolites. Primary metabolites have a function that is essential to the survival of the organism that produces them. Secondary metabolites in contrast have a function that mainly affects other organisms. Secondary metabolites are not essential to survival but do increase the competitiveness of the organism within its environment, because of their ability to modulate biochemical and signal transduction pathways, some secondary metabolites have useful medicinal properties. Natural products especially within the field of chemistry are often defined as primary and secondary metabolites. A more restrictive definition limiting natural products to secondary metabolites is commonly used within the fields of medicinal chemistry, primary metabolites as defined by Kossel are components of basic metabolic pathways that are required for life. They are associated with cellular functions such as nutrient assimilation, energy production. They have a species distribution that span many phyla and frequently more than one kingdom. Primary metabolites include carbohydrates, lipids, amino acids, and nucleic acids which are the building blocks of life

8.
Endogenous opioid
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Opioid peptides are peptides that bind to opioid receptors in the brain, opiates and opioids mimic the effect of these peptides. Such peptides may be produced by the body itself, for example endorphins, the effects of these peptides vary, but they all resemble those of opiates. Brain opioid peptide systems are known to play an important role in motivation, emotion, attachment behaviour, the response to stress and pain, opioid-like peptides may also be absorbed from partially digested food. The opioid food peptides have lengths of typically 4–8 amino acids, the bodys own opioids are generally much longer. Opioid peptides are released by post-translational proteolytic cleavage of precursor proteins, sequence analysis reveals that the conserved N-terminal region of the precursors contains 6 cysteines, which are probably involved in disulfide bond formation. It is speculated that this region might be important for neuropeptide processing, the human genome contains several homologous genes that are known to code for endogenous opioid peptides. The nucleotide sequence of the gene for proopiomelanocortin was characterized in 1980. The POMC gene codes for endogenous opioids such as β-endorphin and gamma-endorphin, the peptides with opioid activity that are derived from proopiomelanocortin comprise the class of endogenous opioid peptides called endorphins. The human gene for the enkephalins was isolated and its described in 1982. The human gene for dynorphins was isolated and its described in 1983. The PNOC gene encoding prepronociceptin, which is cleaved into nociceptin, adrenorphin, amidorphin, and leumorphin were discovered in the 1980s. The endomorphins were discovered in the 1990s, hemorphins, hemoglobin-derived opioid peptides, including hemorphin-4, valorphin, and spinorphin, among others. While not peptides, codeine and morphine are also produced in the human body

9.
Peptide
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Peptides are biologically occurring short chains of amino acid monomers linked by peptide bonds. The covalent chemical bonds are formed when the group of one amino acid reacts with the amine group of another. The shortest peptides are dipeptides, consisting of 2 amino acids joined by a peptide bond, followed by tripeptides, tetrapeptides. A polypeptide is a long, continuous, and unbranched peptide chain, hence, peptides fall under the broad chemical classes of biological oligomers and polymers, alongside nucleic acids, oligosaccharides and polysaccharides, etc. Peptides are distinguished from proteins on the basis of size, all peptides except cyclic peptides have an N-terminal and C-terminal residue at the end of the peptide. Ribosomal peptides Ribosomal peptides are synthesized by translation of mRNA and they are often subjected to proteolysis to generate the mature form. These function, typically in higher organisms, as hormones and signaling molecules, some organisms produce peptides as antibiotics, such as microcins. Since they are translated, the amino acid residues involved are restricted to those utilized by the ribosome, however, these peptides frequently have posttranslational modifications such as phosphorylation, hydroxylation, sulfonation, palmitoylation, glycosylation and disulfide formation. In general, they are linear, although lariat structures have been observed, more exotic manipulations do occur, such as racemization of L-amino acids to D-amino acids in platypus venom. Nonribosomal peptides Nonribosomal peptides are assembled by enzymes that are specific to each peptide, the most common non-ribosomal peptide is glutathione, which is a component of the antioxidant defenses of most aerobic organisms. Other nonribosomal peptides are most common in organisms, plants. These complexes are often out in a similar fashion. These peptides are often cyclic and can have highly complex cyclic structures, since the system is closely related to the machinery for building fatty acids and polyketides, hybrid compounds are often found. The presence of oxazoles or thiazoles often indicates that the compound was synthesized in this fashion, Peptones See also Tryptone Peptones are derived from animal milk or meat digested by proteolysis. In addition to containing small peptides, the material includes fats, metals, salts, vitamins. Peptones are used in nutrient media for growing bacteria and fungi, Peptide fragments Peptide fragments refer to fragments of proteins that are used to identify or quantify the source protein. Peptides received prominence in molecular biology for several reasons, the first is that peptides allow the creation of peptide antibodies in animals without the need of purifying the protein of interest. This involves synthesizing antigenic peptides of sections of the protein of interest and these will then be used to make antibodies in a rabbit or mouse against the protein

10.
Proteolytic
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Proteolysis is the breakdown of proteins into smaller polypeptides or amino acids. Uncatalysed, the hydrolysis of peptide bonds is extremely slow, taking hundreds of years, proteolysis is typically catalysed by cellular enzymes called proteases, but may also occur by intra-molecular digestion. Low pH or high temperatures can also cause proteolysis non-enzymatically and it is also important in the regulation of some physiological and cellular processes, as well as preventing the accumulation of unwanted or abnormal proteins in cells. Consequently, dis-regulation of proteolysis can cause diseases and is used in some venoms to damage their prey, proteolysis is important as an analytical tool for studying proteins in the laboratory, as well as industrially, for example in food processing and stain removal. Limited proteolysis of a polypeptide during or after translation in protein synthesis often occurs for many proteins and this may involve removal of the N-terminal methionine, signal peptide, and/or the conversion of an inactive or non-functional protein to an active one. The precursor to the functional form of protein is termed proprotein. For example, albumin is first synthesized as preproalbumin and contains a signal peptide. This forms the proalbumin after the signal peptide is cleaved, the initiating methionine may be removed during translation of the nascent protein. For E. coli, fMet is efficiently removed if the second residue is small and uncharged, in both prokaryotes and eukaryotes, the exposed N-terminal residue may determine the half-life of the protein according to the N-end rule. Proteins that are to be targeted to a particular organelle or for secretion have an N-terminal signal peptide directs the protein to its final destination. This signal peptide is removed by proteolysis after their transport through a membrane, the polyprotein pro-opiomelanocortin contains many polypeptide hormones. The cleavage pattern of POMC, however, may vary between different tissues, yielding different sets of polypeptide hormones from the same polyprotein, many viruses also produce their proteins initially as a single polypeptide chain that were translated from a polycistronic mRNA. This polypeptide is subsequently cleaved into individual polypeptide chains, many proteins and hormones are synthesized in the form of their precursors - zymogens, proenzymes, and prehormones. These proteins are cleaved to form their final active structures, insulin, for example, is synthesized as preproinsulin, which yields proinsulin after the signal peptide has been cleaved. The proinsulin is then cleaved at two positions to yield two polypeptide chains linked by two disulfide bonds, removal of two C-terminal residues from the B-chain then yields the mature insulin. Proteases in particular are synthesized in the form so that they may be safely stored in cells. This is to ensure that the protease is activated only in the location or context. Proteolysis can, therefore, be a method of regulating biological processes by turning inactive proteins into active ones, a good example is the blood clotting cascade whereby an initial event triggers a cascade of sequential proteolytic activation of many specific proteases, resulting in blood coagulation

11.
Residue (chemistry)
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In chemistry residue is whatever remains or acts as a contaminant after a given class of events. Residue may be the material remaining after a process of preparation, separation, or purification, such as distillation, evaporation and it may also denote the undesired by-products of a chemical reaction. Toxic chemical residues, wastes or contamination from other processes, are a concern in food safety, for example, the U. S. Food and Drug Administration and the Canadian Food Inspection Agency have guidelines for detecting chemical residues that are possibly dangerous to consume. Residue may refer to an atom or a group of atoms that forms part of a molecule, in biochemistry and molecular biology, a residue refers to a specific monomer within the polymeric chain of a polysaccharide, protein or nucleic acid. One might say, This protein consists of 118 amino acid residues or The histidine residue is considered to be basic because it contains an imidazole ring. Note that a residue is different from a moiety, which, a residue might be one amino acid in a polypeptide or one monosaccharide in a starch molecule

12.
Amino acid
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Amino acids are organic compounds containing amine and carboxyl functional groups, along with a side chain specific to each amino acid. The key elements of an acid are carbon, hydrogen, oxygen. About 500 amino acids are known and can be classified in many ways, in the form of proteins, amino acids comprise the second-largest component of human muscles, cells and other tissues. Outside proteins, amino acids perform critical roles in such as neurotransmitter transport. In biochemistry, amino acids having both the amine and the acid groups attached to the first carbon atom have particular importance. They are known as 2-, alpha-, or α-amino acids and they include the 22 proteinogenic amino acids, which combine into peptide chains to form the building-blocks of a vast array of proteins. These are all L-stereoisomers, although a few D-amino acids occur in bacterial envelopes, as a neuromodulator, twenty of the proteinogenic amino acids are encoded directly by triplet codons in the genetic code and are known as standard amino acids. The other two are selenocysteine, and pyrrolysine, pyrrolysine and selenocysteine are encoded via variant codons, for example, selenocysteine is encoded by stop codon and SECIS element. N-formylmethionine is generally considered as a form of methionine rather than as a separate proteinogenic amino acid, codon–tRNA combinations not found in nature can also be used to expand the genetic code and create novel proteins known as alloproteins incorporating non-proteinogenic amino acids. Many important proteinogenic and non-proteinogenic amino acids also play critical roles within the body. Nine proteinogenic amino acids are called essential for humans because they cannot be created from other compounds by the human body, others may be conditionally essential for certain ages or medical conditions. Essential amino acids may also differ between species, because of their biological significance, amino acids are important in nutrition and are commonly used in nutritional supplements, fertilizers, and food technology. Industrial uses include the production of drugs, biodegradable plastics, the first few amino acids were discovered in the early 19th century. In 1806, French chemists Louis-Nicolas Vauquelin and Pierre Jean Robiquet isolated a compound in asparagus that was subsequently named asparagine, cystine was discovered in 1810, although its monomer, cysteine, remained undiscovered until 1884. Glycine and leucine were discovered in 1820, usage of the term amino acid in the English language is from 1898. Proteins were found to yield amino acids after enzymatic digestion or acid hydrolysis, in the structure shown at the top of the page, R represents a side chain specific to each amino acid. The carbon atom next to the group is called the α–carbon. Amino acids containing an amino group bonded directly to the alpha carbon are referred to as amino acids

13.
Protein primary structure
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Protein primary structure is the linear sequence of amino acids in a peptide or protein. By convention, the structure of a protein is reported starting from the amino-terminal end to the carboxyl-terminal end. Protein biosynthesis is most commonly performed by ribosomes in cells, peptides can also be synthesised in the laboratory. Protein primary structures can be sequenced, or inferred from DNA sequences. Amino acids are polymerised via peptide bonds to form a long backbone, in biological systems, proteins are produced during translation by a cells ribosomes. Some organisms can also make short peptides by non-ribosomal peptide synthesis, which often use amino acids other than the standard 20, peptides can be synthesised chemically via a range of laboratory methods. Chemical methods typically synthesise peptides in the order to biological protein synthesis. Protein sequence is typically notated as a string of letters, listing the amino acids starting at the end through to the carboxyl-terminal end. Either a three letter code or single letter code can be used to represent the 20 naturally occurring amino acids, peptides can be directly sequenced, or inferred from DNA sequences. Large sequence databases now exist that collate known protein sequences, in general, polypeptides are unbranched polymers, so their primary structure can often be specified by the sequence of amino acids along their backbone. The chiral centers of a chain can undergo racemization. Although it does not change the sequence, it affect the chemical properties of the sequence. In particular, the L-amino acids normally found in proteins can spontaneously isomerize at the C α atom to form D-amino acids, additionally, proline can form stable trans-isomers at the peptide bond. Finally, the protein can undergo a variety of posttranslational modifications, formylation − C H The N-terminal methionine usually found after translation has an N-terminus blocked with a formyl group. This formyl group is removed by the enzyme deformylase, pyroglutamate An N-terminal glutamine can attack itself, forming a cyclic pyroglutamate group. Myristoylation − C −12 − C H3 Similar to acetylation, instead of a simple methyl group, the myristoyl group has a tail of 14 hydrophobic carbons, which make it ideal for anchoring proteins to cellular membranes. The C-terminal carboxylate group of a polypeptide can also be modified, Glycosyl phosphatidylinositol attachment Glycosyl phosphatidylinositol is a large, hydrophobic phospholipid prosthetic group that achors proteins to cellular membranes. It is attached to the polypeptide C-terminus through a linkage that then connects to ethanolamine, thence to sundry sugars

14.
Pitrilysin metallopeptidase 1
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Pitrilysin metallopeptidase 1 also known as presequence protease, mitochondrial and metalloprotease 1 is an enzyme that in humans is encoded by the PITRM1 gene. It is also sometimes called metalloprotease 1. PreP facilitates proteostasis by utilizing an ~13300-A catalytic chamber to degrade toxic peptides, including mitochondrial presequences, deficiency of PreP is found associated with Alzheimer’s disease. The PITRM1 gene is located at chromosome 10q15.2, consisting of 28 exons, PreP is a 117 kDa M16C enzyme that is widely expressed in human tissues. PreP is composed of PreP-N and PreP-C domains, which are connected by a helical hairpin. Its structure demonstrates that substrate selection by size-exclusion is a mechanism in M16C proteases. PreP is an Zn2+-dependent and ATP-independent metalloprotease, it doesn’t select substrates on the basis of post-translational modifications or embedded degradation tags, instead, it uses a negatively charged catalytic chamber to engulf substrates peptides of up to ~65 residues while excluding larger, folded proteins. It primarily localizes to the matrix, and cuts a range of peptides into recyclable fragments. The substrates of PreP are vital to proteostasis, as they can insert to mitochondrial membranes, disrupting electrical potential, thus deletion of PRTRM1 leads to a delayed growth phenotype. Notabley, PreP degrades several functionally relevant Aβ species, the aggregates of which are toxic to the neuron, PreP is the Aβ-degrading protease in mitochondria. Immune-depletion of PreP in brain mitochondria prevents degradation of mitochondrial Aβ, a recent study also suggests that PreP regulates islet amyloid polypeptide in beta cells. PITRM1 has been shown to interact with the proteins, CCL22, CGB2, DDX41, DEFB104A, HDHD3, MRPL12, NDUFV2, PRDX6, PRKCSH, RARS2, RIF1, SUCLG2, TEKT3, TERF2. Model organisms have been used in the study of PITRM1 function, a conditional knockout mouse line called Pitrm1tm1aWtsi was generated at the Wellcome Trust Sanger Institute. Male and female animals underwent a standardized phenotypic screen to determine the effects of deletion, additional screens performed, - In-depth immunological phenotyping

15.
Enzyme
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Enzymes /ˈɛnzaɪmz/ are macromolecular biological catalysts. Enzymes accelerate, or catalyze, chemical reactions, the molecules at the beginning of the process upon which enzymes may act are called substrates and the enzyme converts these into different molecules, called products. Almost all metabolic processes in the cell need enzymes in order to occur at rates fast enough to sustain life, the set of enzymes made in a cell determines which metabolic pathways occur in that cell. The study of enzymes is called enzymology, enzymes are known to catalyze more than 5,000 biochemical reaction types. Most enzymes are proteins, although a few are catalytic RNA molecules, enzymes specificity comes from their unique three-dimensional structures. Like all catalysts, enzymes increase the rate of a reaction by lowering its activation energy, some enzymes can make their conversion of substrate to product occur many millions of times faster. An extreme example is orotidine 5-phosphate decarboxylase, which allows a reaction that would take millions of years to occur in milliseconds. Chemically, enzymes are like any catalyst and are not consumed in chemical reactions, enzymes differ from most other catalysts by being much more specific. Enzyme activity can be affected by other molecules, inhibitors are molecules that decrease enzyme activity, many drugs and poisons are enzyme inhibitors. An enzymes activity decreases markedly outside its optimal temperature and pH, some enzymes are used commercially, for example, in the synthesis of antibiotics. French chemist Anselme Payen was the first to discover an enzyme, diastase and he wrote that alcoholic fermentation is an act correlated with the life and organization of the yeast cells, not with the death or putrefaction of the cells. In 1877, German physiologist Wilhelm Kühne first used the term enzyme, the word enzyme was used later to refer to nonliving substances such as pepsin, and the word ferment was used to refer to chemical activity produced by living organisms. Eduard Buchner submitted his first paper on the study of yeast extracts in 1897, in a series of experiments at the University of Berlin, he found that sugar was fermented by yeast extracts even when there were no living yeast cells in the mixture. He named the enzyme that brought about the fermentation of sucrose zymase, in 1907, he received the Nobel Prize in Chemistry for his discovery of cell-free fermentation. Following Buchners example, enzymes are usually named according to the reaction they carry out, the biochemical identity of enzymes was still unknown in the early 1900s. Sumner showed that the enzyme urease was a protein and crystallized it. These three scientists were awarded the 1946 Nobel Prize in Chemistry, the discovery that enzymes could be crystallized eventually allowed their structures to be solved by x-ray crystallography. This high-resolution structure of lysozyme marked the beginning of the field of structural biology, an enzymes name is often derived from its substrate or the chemical reaction it catalyzes, with the word ending in -ase

16.
Agonist
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An agonist is a chemical that binds to a receptor and activates the receptor to produce a biological response. Whereas an agonist causes an action, an antagonist blocks the action of the agonist, receptors can be activated by either endogenous or exogenous agonists, resulting in a biological response. A physiological agonist is a substance that creates the same bodily responses but does not bind to the same receptor, an endogenous agonist for a particular receptor is a compound naturally produced by the body that binds to and activates that receptor. For example, the endogenous agonist for serotonin receptors is serotonin, a superagonist is a compound that is capable of producing a greater maximal response than the endogenous agonist for the target receptor, and thus has an efficacy of more than 100%. Full agonists bind and activate a receptor, producing full efficacy at that receptor, one example of a drug that acts as a full agonist is isoproterenol, which mimics the action of adrenaline at β adrenoreceptors. Another example is morphine, which mimics the actions of endorphins at μ-opioid receptors throughout the nervous system. Partial agonists also bind and activate a receptor, but have only partial efficacy at the receptor relative to a full agonist. Agents like buprenorphine are used to treat opiate dependence for this reason, as they produce milder effects on the receptor with lower dependence. An inverse agonist is an agent that binds to the same receptor binding-site as an agonist for that receptor, inverse agonists exert the opposite pharmacological effect of a receptor agonist, not merely an absence of the agonist effect as seen with antagonist. An example is the inverse agonist rimonabant. A co-agonist works with other co-agonists to produce the desired effect together, NMDA receptor activation requires the binding of both glutamate, glycine and D-serine co-agonists. An irreversible agonist is a type of agonist that binds permanently to a receptor through the formation of covalent bonds, a few of these have been described. A selective agonist is selective for a type of receptor. E. g. buspirone is a selective agonist for serotonin 5-HT1A, terms that describe this phenomenon are functional selectivity, protean agonism, or selective receptor modulators. Potency is the amount of agonist needed to elicit a desired response, the potency of an agonist is inversely related to its EC50 value. The EC50 can be measured for a given agonist by determining the concentration of agonist needed to elicit half of the biological response of the agonist. The EC50 value is useful for comparing the potency of drugs with similar efficacies producing physiologically similar effects, the smaller the EC50 value, the greater the potency of the agonist, the lower the concentration of drug that is required to elicit the maximum biological response. This relationship, termed the index, is defined as the ratio TD50, ED50

17.
Opioid peptide
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Opioid peptides are peptides that bind to opioid receptors in the brain, opiates and opioids mimic the effect of these peptides. Such peptides may be produced by the body itself, for example endorphins, the effects of these peptides vary, but they all resemble those of opiates. Brain opioid peptide systems are known to play an important role in motivation, emotion, attachment behaviour, the response to stress and pain, opioid-like peptides may also be absorbed from partially digested food. The opioid food peptides have lengths of typically 4–8 amino acids, the bodys own opioids are generally much longer. Opioid peptides are released by post-translational proteolytic cleavage of precursor proteins, sequence analysis reveals that the conserved N-terminal region of the precursors contains 6 cysteines, which are probably involved in disulfide bond formation. It is speculated that this region might be important for neuropeptide processing, the human genome contains several homologous genes that are known to code for endogenous opioid peptides. The nucleotide sequence of the gene for proopiomelanocortin was characterized in 1980. The POMC gene codes for endogenous opioids such as β-endorphin and gamma-endorphin, the peptides with opioid activity that are derived from proopiomelanocortin comprise the class of endogenous opioid peptides called endorphins. The human gene for the enkephalins was isolated and its described in 1982. The human gene for dynorphins was isolated and its described in 1983. The PNOC gene encoding prepronociceptin, which is cleaved into nociceptin, adrenorphin, amidorphin, and leumorphin were discovered in the 1980s. The endomorphins were discovered in the 1990s, hemorphins, hemoglobin-derived opioid peptides, including hemorphin-4, valorphin, and spinorphin, among others. While not peptides, codeine and morphine are also produced in the human body

18.
PubMed Identifier
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PubMed is a free search engine accessing primarily the MEDLINE database of references and abstracts on life sciences and biomedical topics. The United States National Library of Medicine at the National Institutes of Health maintains the database as part of the Entrez system of information retrieval, from 1971 to 1997, MEDLINE online access to the MEDLARS Online computerized database primarily had been through institutional facilities, such as university libraries. PubMed, first released in January 1996, ushered in the era of private, free, home-, the PubMed system was offered free to the public in June 1997, when MEDLINE searches via the Web were demonstrated, in a ceremony, by Vice President Al Gore. Information about the journals indexed in MEDLINE, and available through PubMed, is found in the NLM Catalog. As of 5 January 2017, PubMed has more than 26.8 million records going back to 1966, selectively to the year 1865, and very selectively to 1809, about 500,000 new records are added each year. As of the date,13.1 million of PubMeds records are listed with their abstracts. In 2016, NLM changed the system so that publishers will be able to directly correct typos. Simple searches on PubMed can be carried out by entering key aspects of a subject into PubMeds search window, when a journal article is indexed, numerous article parameters are extracted and stored as structured information. Such parameters are, Article Type, Secondary identifiers, Language, publication type parameter enables many special features. As these clinical girish can generate small sets of robust studies with considerable precision, since July 2005, the MEDLINE article indexing process extracts important identifiers from the article abstract and puts those in a field called Secondary Identifier. The secondary identifier field is to store numbers to various databases of molecular sequence data, gene expression or chemical compounds. For clinical trials, PubMed extracts trial IDs for the two largest trial registries, ClinicalTrials. gov and the International Standard Randomized Controlled Trial Number Register, a reference which is judged particularly relevant can be marked and related articles can be identified. If relevant, several studies can be selected and related articles to all of them can be generated using the Find related data option, the related articles are then listed in order of relatedness. To create these lists of related articles, PubMed compares words from the title and abstract of each citation, as well as the MeSH headings assigned, using a powerful word-weighted algorithm. The related articles function has been judged to be so precise that some researchers suggest it can be used instead of a full search, a strong feature of PubMed is its ability to automatically link to MeSH terms and subheadings. Examples would be, bad breath links to halitosis, heart attack to myocardial infarction, where appropriate, these MeSH terms are automatically expanded, that is, include more specific terms. Terms like nursing are automatically linked to Nursing or Nursing and this important feature makes PubMed searches automatically more sensitive and avoids false-negative hits by compensating for the diversity of medical terminology. The My NCBI area can be accessed from any computer with web-access, an earlier version of My NCBI was called PubMed Cubby

19.
International Standard Book Number
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The International Standard Book Number is a unique numeric commercial book identifier. An ISBN is assigned to each edition and variation of a book, for example, an e-book, a paperback and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, the method of assigning an ISBN is nation-based and varies from country to country, often depending on how large the publishing industry is within a country. The initial ISBN configuration of recognition was generated in 1967 based upon the 9-digit Standard Book Numbering created in 1966, the 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108. Occasionally, a book may appear without a printed ISBN if it is printed privately or the author does not follow the usual ISBN procedure, however, this can be rectified later. Another identifier, the International Standard Serial Number, identifies periodical publications such as magazines, the ISBN configuration of recognition was generated in 1967 in the United Kingdom by David Whitaker and in 1968 in the US by Emery Koltay. The 10-digit ISBN format was developed by the International Organization for Standardization and was published in 1970 as international standard ISO2108, the United Kingdom continued to use the 9-digit SBN code until 1974. The ISO on-line facility only refers back to 1978, an SBN may be converted to an ISBN by prefixing the digit 0. For example, the edition of Mr. J. G. Reeder Returns, published by Hodder in 1965, has SBN340013818 -340 indicating the publisher,01381 their serial number. This can be converted to ISBN 0-340-01381-8, the check digit does not need to be re-calculated, since 1 January 2007, ISBNs have contained 13 digits, a format that is compatible with Bookland European Article Number EAN-13s. An ISBN is assigned to each edition and variation of a book, for example, an ebook, a paperback, and a hardcover edition of the same book would each have a different ISBN. The ISBN is 13 digits long if assigned on or after 1 January 2007, a 13-digit ISBN can be separated into its parts, and when this is done it is customary to separate the parts with hyphens or spaces. Separating the parts of a 10-digit ISBN is also done with either hyphens or spaces, figuring out how to correctly separate a given ISBN number is complicated, because most of the parts do not use a fixed number of digits. ISBN issuance is country-specific, in that ISBNs are issued by the ISBN registration agency that is responsible for country or territory regardless of the publication language. Some ISBN registration agencies are based in national libraries or within ministries of culture, in other cases, the ISBN registration service is provided by organisations such as bibliographic data providers that are not government funded. In Canada, ISBNs are issued at no cost with the purpose of encouraging Canadian culture. In the United Kingdom, United States, and some countries, where the service is provided by non-government-funded organisations. Australia, ISBNs are issued by the library services agency Thorpe-Bowker

20.
Neuropeptide
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Neuropeptides are small protein-like molecules used by neurons to communicate with each other. They are neuronal signaling molecules that influence the activity of the brain, different neuropeptides are involved in a wide range of brain functions, including analgesia, reward, food intake, metabolism, reproduction, social behaviors, learning and memory. Neuropeptides are related to peptide hormones, and in some cases peptides that function in the periphery as hormones also have functions as neuropeptides. In contrast, peptide hormones are secreted from cells and travel through the blood to distant tissues where they evoke a response. Neuropeptides modulate neuronal communication by acting on cell surface receptors, many neuropeptides are co-released with other small-molecule neurotransmitters. The human genome contains about 90 genes that encode precursors of neuropeptides, at present about 100 different peptides are known to be released by different populations of neurons in the mammalian brain. Neurons use many different chemical signals to communicate information, including neurotransmitters, peptides, peptides are unique among these cell-cell signaling molecules in several respects. One major difference is that peptides are not recycled back into the cell once secreted and these extracellular processing events add to the complexity of neuropeptides as cell-cell signaling molecules. Many populations of neurons have distinctive biochemical phenotypes and these peptides are all released centrally and act on other neurons at specific receptors. The neuropeptide Y neurons also make the classical inhibitory neurotransmitter GABA, peptide signals play a role in information processing that is different from that of conventional neurotransmitters, and many appear to be particularly associated with specific behaviours. For example, oxytocin and vasopressin have striking and specific effects on social behaviours, including maternal behaviour, generally, peptides act at metabotropic or G-protein-coupled receptors expressed by selective populations of neurons. In essence they act as signals between one population of neurons and another. Neurotransmitters generally affect the excitability of neurons, by depolarising them or by hyperpolarising them. Peptides have much more effects, amongst other things, they can affect gene expression, local blood flow, synaptogenesis. Peptides tend to have prolonged actions, and some have striking effects on behaviour, neurons very often make both a conventional neurotransmitter and one or more neuropeptides. The following is a list of neuroactive peptides coexisting with other neurotransmitters, transmitter names are shown in bold. A2006 discovery might have important implications for treatment of diabetes, researchers at the Toronto Hospital for Sick Children injected capsaicin into NOD mice to kill the pancreatic sensory nerves. This treatment reduced the development of diabetes in mice by 80%

21.
Endomorphin-2
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Endomorphin-2 is an endogenous opioid peptide and one of the two endomorphins. It is an affinity, highly selective agonist of the μ-opioid receptor. Like EM-1, EM-2 produces analgesia in animals, but whereas EM-1 is more prevalent in the brain, moreover, while EM-1 produces conditioned place preference, a measure of drug reward, EM-2 produces conditioned place aversion, an effect which is dynorphin A-dependent. Similarly to the case of EM-1, the encoding for EM-2 has not yet been identified

22.
Beta-Endorphin
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β-Endorphin is an endogenous opioid neuropeptide found in the neurons of both the central and peripheral nervous system. It is one of five endorphins found in humans, the others of which include α-endorphin, γ-endorphin, α-neoendorphin, the amino acid sequence is, Tyr-Gly-Gly-Phe-Met-Thr-Ser-Glu-Lys-Ser-Gln-Thr-Pro-Leu-Val-Thr-Leu-Phe-Lys-Asn-Ala-Ile-Ile-Lys-Asn-Ala-Tyr-Lys-Lys-Gly-Glu. The first 16 amino acids are identical to α-Endorphin, β-Endorphin is a peptide,31 amino acids long, resulting from processing of the precursor proopiomelanocortin. β-Endorphin is found in neurons of the hypothalamus, as well as the pituitary gland, β-Endorphin was discovered in camel pituitary extracts by C. H. It is used as an analgesic in the body to numb or dull pains and that is the reason why humans start to feel better immediately after an acute physical trauma even though the symptoms are still present. The reason the pain dulls is because it binds to and activates opioid receptors, β-Endorphin has approximately 18 to 33 times the analgesic potency of morphine, though its hormonal effect is species dependent. β-Endorphin release in response to exercise has been known and studied since at least the 1980s, studies have demonstrated that serum concentrations of endogenous opioids, in particular β-endorphin and β-lipotrophin, increase in response to both acute exercise and training. The release of β-endorphin during exercise is associated with a phenomenon known in popular culture as a runners high. CID16132316 from PubChem - β-endorphin CID3081525 from PubChem - β-endorphin CID133304 from PubChem - β-endorphin β-endorphin at the US National Library of Medicine Medical Subject Headings

23.
Gamma-Endorphin
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γ-Endorphin is an opioid peptide that is characterized by the presence of 17 amino acids. The first 16 amino acids are identical to α-endorphin with Leucine added at the end, similar to other endorphins, research focusing upon γ-endorphin has been ongoing since its discovery in the 1970s. Yet, most of the information about the exact role within the body is speculation that has yet to be proven. Further research is needed, but if γ-endorphin does indeed possess such characteristics, the substance could eventually be utilized as a useful means of medical treatment

24.
Enkephalin
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An enkephalin is a pentapeptide involved in regulating nociception in the body. The enkephalins are termed endogenous ligands, as they are internally derived, discovered in 1975, two forms of enkephalin were discovered, one containing leucine, and the other containing methionine. Both are products of the proenkephalin gene, there are three well-characterized families of opioid peptides produced by the body, enkephalins, endorphins, and dynorphins. The met-enkephalin peptide sequence is coded for by the enkephalin gene, the proopiomelanocortin gene also contains the met-enkephalin sequence on the N-terminus of beta-endorphin, but the endorphin peptide is not processed into enkephalin. The receptors for enkephalin are the opioid receptors and mu opioid receptors. Opioid receptors are a group of G-protein-coupled receptors, with opioids as ligands as well. The other endogenous opioids are dynorphins, endorphins, endomorphins, the opioid receptors are ~40% identical to somatostatin receptors. Endorphin Opioid peptide Racecadotril RB-101 Enkephalins at the US National Library of Medicine Medical Subject Headings Physiology, 6/6ch2/s6ch2_36 - Essentials of Human Physiology

25.
Leu-enkephalin
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Leu-enkephalin is an endogenous opioid peptide neurotransmitter with the amino acid sequence Tyr-Gly-Gly-Phe-Leu that is found naturally in the brains of many animals, including humans. It is one of the two forms of enkephalin, the other is met-enkephalin, the tyrosine residue at position 1 is thought to be analogous to the 3-hydroxyl group on morphine. Leu-enkephalin has agonistic actions at both the μ- and δ-opioid receptors, with significantly greater preference for the latter and it has little to no effect on the κ-opioid receptor

26.
Hemorphin-4
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Hemorphin-4 is an endogenous opioid peptide of the hemorphin family which possesses antinociceptive properties and is derived from the β-chain of hemoglobin in the bloodstream. It is a tetrapeptide with the amino acid sequence Tyr-Pro-Trp-Thr and it acts as an agonist at these sites. Hemorphin-4 also has effects on angiotensin-converting enzyme, and as a result. Notably, inhibition of ACE also reduces enkephalin catabolism

The energies of the stages of a chemical reaction. Uncatalysed (dashed line), substrates need a lot of activation energy to reach a transition state, which then decays into lower-energy products. When enzyme catalysed (solid line), the enzyme binds the substrates (ES), then stabilizes the transition state (ES‡) to reduce the activation energy required to produce products (EP) which are finally released.

β-Endorphin is an endogenous opioid neuropeptide and peptide hormone that is produced in certain neurons within the …

This diagram depicts the formation of β-endorphin from the proopiomelanocortin gene in the pituitary gland. Portions of the second and third exon of this gene make up the proopiomelanocortin protein. The cleavage of the C-terminal end of this protein produces β-lipotropin, which is then cleaved again to form β-endorphin. The proopiomelanocortin protein is also a precursor to other neuropeptides and hormones, such as adrenocorticotropic hormone.